ǂa ǂpipeline for identification of polymorphic microsatellites loci within assemblies of related species
Ante Turudić (Author), Zlatko Liber (Author), Martina Grdiša (Author), Jernej Jakše (Author), Filip Varga (Author), Igor Poljak (Author), Zlatko Šatović (Author)

Abstract

Simple sequence repeats (SSRs) have become one of the most popular molecular markers and are used in numerous fields, including conservation genetics, population genetic studies, and genetic mapping. Advances in next-generation sequencing technology and the growing amount of genomic data are driving the development of bioinformatics tools for SSR marker design. These tools work with different combinations of input data, which can be raw reads or assemblies, and with one or more input datasets. We present here a new strategy and implementation of a simple standalone pipeline that utilizes more than one assembly for the in silico design of PCR primers for microsatellite loci in more than one species. Primers are tested in silico to determine if they are polymorphic, eliminating the need to test time-consuming cross-species amplification in the laboratory. The end result is a set of markers that are in silico polymorphic in all analyzed species and have great potential for the identification of interspecies hybrids. The efficiency of the tool is demonstrated using two examples at different taxonomic levels and with different numbers of input assemblies to generate promising, high-quality SSR markers.

Keywords

SSRs;NGS;SSR primer design;in silico PCR;

Data

Language: English
Year of publishing:
Typology: 1.01 - Original Scientific Article
Organization: UL BF - Biotechnical Faculty
UDC: 577.2
COBISS: 196357123 Link will open in a new window
ISSN: 1422-0067
Views: 31
Downloads: 7
Average score: 0 (0 votes)
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Other data

Secondary language: Slovenian
Secondary keywords: bioinformatika;molekularna genetika;molekularni markerji;mikrosateliti;SSR markerji;genom;
Type (COBISS): Article
Pages: 10 str.
Volume: ǂVol. ǂ25
Issue: ǂiss. ǂ6, art. 3169
Chronology: 2024
DOI: 10.3390/ijms25063169
ID: 23769224
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